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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ), 'gf_id' => 'HOM05D001248', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001248' ), 'data_identifier' => 'HOM05D001248', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001248', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '499', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13120' => 'bna', 'A02p32700' => 'bna', 'A03p52970' => 'bna', 'A05p26120' => 'bna', 'A06p10580' => 'bna', 'A09p23860' => 'bna', 'Aa31LG1G530' => 'aar', 'Aa31LG2G7760' => 'aar', 'Aa31LG6G3770' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1500' => 'aag', 'Actinidia05524' => 'ach', 'Actinidia11775' => 'ach', 'Actinidia26926' => 'ach', 'Actinidia30190' => 'ach', 'Ah.01g022320' => 'amhyb', 'Ah.02g120690' => 'amhyb', 'Ah.03g147580' => 'amhyb', 'Ah.04g165760' => 'amhyb', 'Ah.06g185670' => 'amhyb', 'Ah.09g235040' => 'amhyb', 'AL1G26500' => 'aly', 'AL1G60380' => 'aly', 'AL5G11460' => 'aly', 'AL7G32140' => 'aly', 'Aqoxy1G03272' => 'aox', 'Aqoxy3G04218' => 'aox', 'Aqoxy6G00775' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Z5YS0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24AKL2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5C07ZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6BSH1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A6I4VR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F30MHA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FJ2VI4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE4UL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRA99Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KAI8DY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L23BE1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R1I8D9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z5ZDSF' => 'arhy', 'AT1G14530' => 'ath', 'AT2G02180' => 'ath', 'AT4G21790' => 'ath', 'ATR0618G238' => 'atr', 'ATR0752G062' => 'atr', 'ATR0782G110' => 'atr', 'Atru.chr10.2186' => 'acertr', 'Atru.chr11.1084' => 'acertr', 'AUR62003528' => 'cqu', 'AUR62010139' => 'cqu', 'AUR62012680' => 'cqu', 'AUR62013132' => 'cqu', 'AUR62015739' => 'cqu', 'AUR62017842' => 'cqu', 'AUR62020471' => 'cqu', 'AUR62021976' => 'cqu', 'BcaB02g06510' => 'bca', 'BcaB07g30351' => 'bca', 'BcaB07g30702' => 'bca', 'BcaC03g17122' => 'bca', 'BcaC04g21527' => 'bca', 'BcaC05g25362' => 'bca', 'BcaC05g29323' => 'bca', 'BcaC06g30680' => 'bca', 'BcaC09g51201' => 'bca', 'BcaC09g51202' => 'bca', 'BcaNung00833' => 'bca', 'BcaNung02247' => 'bca', 'BolC1t00638H' => 'bol', 'BolC1t01534H' => 'bol', 'BolC1t01535H' => 'bol', 'BolC2t11114H' => 'bol', 'BolC3t13446H' => 'bol', 'BolC3t19624H' => 'bol', 'BolC5t29991H' => 'bol', 'BolC7t45638H' => 'bol', 'BolC8t52118H' => 'bol', 'BolC9t55907H' => 'bol', 'BolC9t55935H' => 'bol', 'BraA01t01255Z' => 'bra', 'BraA01t01256Z' => 'bra', 'BraA02t08285Z' => 'bra', 'BraA03t14371Z' => 'bra', 'BraA06t24238Z' => 'bra', 'BraA09t37991Z' => 'bra', 'BraA09t41569Z' => 'bra', 'C01p15810' => 'bna', 'C02p24410' => 'bna', 'C02p50320' => 'bna', 'C03p73280' => 'bna', 'C05p12450' => 'bna', 'C07p51400' => 'bna', 'C09p10760' => 'bna', 'C09p30710' => 'bna', 'CAN.G105.17' => 'can', 'CAN.G282.82' => 'can', 'CAN.G458.4' => 'can', 'CAN.G523.64' => 'can', 'CAN.G569.20' => 'can', 'CANSAT56G0591' => 'cansat', 'CANSAT78G1364' => 'cansat', 'CARHR015010' => 'chi', 'CARHR015020' => 'chi', 'CARHR144870' => 'chi', 'CARHR228560' => 'chi', 'Carub.0001s1429' => 'cru', 'Carub.0001s4118' => 'cru', 'Carub.0005s0127' => 'cru', 'Carub.0007s1961' => 'cru', 'Ca_12457_v3' => 'car', 'Ca_18208_v3' => 'car', 'Ca_18356_v3' => 'car', 'Ca_21092_v3' => 'car', 'Ca_30200_v3' => 'car', 'CBR_g20333' => 'cbr', 'CBR_g22030' => 'cbr', 'Cc02_g21500' => 'ccan', 'Cc09_g01860' => 'ccan', 'Cc11_g03250' => 'ccan', 'CDE04G3575' => 'cde', 'CDE05G0050' => 'cde', 'CDE05G0444' => 'cde', 'CDE05G1174' => 'cde', 'CDE08G1073' => 'cde', 'CDE08G1361' => 'cde', 'Cfa000244' => 'cfa', 'Cfa005590' => 'cfa', 'Cfa015111' => 'cfa', 'Cfa015112' => 'cfa', 'Ciclev10016130m.g' => 'ccl', 'Ciclev10021570m.g' => 'ccl', 'Ciclev10030018m.g' => 'ccl', 'CiPaw.05G035000' => 'cil', 'CiPaw.05G164800' => 'cil', 'CiPaw.09G089700' => 'cil', 'CiPaw.10G069700' => 'cil', 'ClCG03G004840' => 'cla', 'ClCG09G015470' => 'cla', 'ClCG11G000820' => 'cla', 'COL.COLO4_08573' => 'col', 'COL.COLO4_27666' => 'col', 'COL.COLO4_31750' => 'col', 'Cpa.g.sc198.34' => 'cpa', 'Cpa.g.sc2.60' => 'cpa', 'Cpa.g.sc42.45' => 'cpa', 'Cre12.g487250' => 'cre', 'CsaV3_1G010880' => 'csa', 'CsaV3_5G012600' => 'csa', 'CsaV3_5G012610' => 'csa', 'CsaV3_5G012810' => 'csa', 'CsaV3_7G006540' => 'csa', 'CSS0000175' => 'camsi', 'CSS0017819' => 'camsi', 'CSS0034601' => 'camsi', 'CSS0039728' => 'camsi', 'CSS0049030' => 'camsi', 'DCAR_002630' => 'dca', 'DCAR_004207' => 'dca', 'DCAR_023510' => 'dca', 'DCAR_029211' => 'dca', 'Dinv12786' => 'din', 'Dinv13876' => 'din', 'Dinv20036' => 'din', 'Dinv24187' => 'din', 'Dinv28158' => 'din', 'Duzib132G0103' => 'dzi', 'Duzib160G0867' => 'dzi', 'Duzib192G0336' => 'dzi', 'Duzib235G1409' => 'dzi', 'Duzib248G1239' => 'dzi', 'Duzib251G0002' => 'dzi', 'Duzib268G1235' => 'dzi', 'ECA233G5098' => 'eca', 'ECA234G4474' => 'eca', 'ECA236G1468' => 'eca', 'ECA240G1016' => 'eca', 'EL10Ac4g07847' => 'bvu', 'EL10Ac6g15352' => 'bvu', 'EL10Ac8g20025' => 'bvu', 'EL10Ac9g21482' => 'bvu', 'Eucgr.A00118' => 'egr', 'Eucgr.D01307' => 'egr', 'Eucgr.E04078' => 'egr', 'Eucgr.G02559' => 'egr', 'FAN07G2915' => 'fan', 'FAN11G2458' => 'fan', 'FAN12G3991' => 'fan', 'FAN16G1767' => 'fan', 'FAN17G2890' => 'fan', 'FAN21G0650' => 'fan', 'FAN21G1804' => 'fan', 'FAN21G3801' => 'fan', 'FAN22G2203' => 'fan', 'FAN25G1592' => 'fan', 'FvH4_3g02360' => 'fve', 'FvH4_3g21800' => 'fve', 'FvH4_4g36360' => 'fve', 'Glyma.02G160700' => 'gma', 'Glyma.05G116900' => 'gma', 'Glyma.05G135900' => 'gma', 'Glyma.07G177000' => 'gma', 'Glyma.07G259300' => 'gma', 'Glyma.08G072000' => 'gma', 'Glyma.08G091200' => 'gma', 'Glyma.17G015000' => 'gma', 'Glyma.20G010800' => 'gma', 'Gohir.A03G174300' => 'ghi', 'Gohir.A04G144400' => 'ghi', 'Gohir.A05G168800' => 'ghi', 'Gohir.A10G013800' => 'ghi', 'Gohir.A12G155600' => 'ghi', 'Gohir.A13G026300' => 'ghi', 'Gohir.A13G067500' => 'ghi', 'Gohir.D02G078700' => 'ghi', 'Gohir.D02G197500' => 'ghi', 'Gohir.D03G069100' => 'ghi', 'Gohir.D04G189000' => 'ghi', 'Gohir.D05G172000' => 'ghi', 'Gohir.D07G175300' => 'ghi', 'Gohir.D08G150350' => 'ghi', 'Gohir.D10G013800' => 'ghi', 'Gohir.D11G246000' => 'ghi', 'Gohir.D12G158800' => 'ghi', 'Gohir.D13G024900' => 'ghi', 'Gohir.D13G054200' => 'ghi', 'Gohir.D13G115432' => 'ghi', 'Gorai.002G150900' => 'gra', 'Gorai.005G220700' => 'gra', 'Gorai.008G171700' => 'gra', 'Gorai.009G177100' => 'gra', 'Gorai.010G079300' => 'gra', 'Gorai.011G015600' => 'gra', 'Gorai.012G184200' => 'gra', 'Gorai.013G028100' => 'gra', 'Gorai.013G061000' => 'gra', 'GSVIVG01001235001' => 'vvi', 'GSVIVG01001243001' => 'vvi', 'GSVIVG01004800001' => 'vvi', 'GSVIVG01005610001' => 'vvi', 'GSVIVG01006094001' => 'vvi', 'GSVIVG01007124001' => 'vvi', 'GSVIVG01010240001' => 'vvi', 'GSVIVG01038795001' => 'vvi', 'HanXRQChr01g0022061' => 'han', 'HanXRQChr03g0065871' => 'han', 'HanXRQChr05g0129611' => 'han', 'HanXRQChr08g0209901' => 'han', 'HanXRQChr09g0240201' => 'han', 'HanXRQChr10g0295901' => 'han', 'HanXRQChr12g0365791' => 'han', 'HanXRQChr14g0446901' => 'han', 'HanXRQChr16g0514421' => 'han', 'HanXRQChr16g0515901' => 'han', 'HanXRQChr16g0516061' => 'han', 'HanXRQChr17g0565541' => 'han', 'Haze_01562' => 'cav', 'Haze_06777' => 'cav', 'Haze_10718' => 'cav', 'Hma1.2p1_0091F.1_g046310' => 'hma', 'Hma1.2p1_0530F.1_g173290' => 'hma', 'Hma1.2p1_0704F.1_g206620' => 'hma', 'Hma1.2p1_1142F.1_g261040' => 'hma', 'HPP92_012837' => 'vpl', 'HPP92_017601' => 'vpl', 'Hund00065' => 'sun', 'Hund02078' => 'sun', 'Hund04376' => 'sun', 'Hund12743' => 'sun', 'Hund15544' => 'sun', 'Hund23261' => 'sun', 'Hund23484' => 'sun', 'Lalb_Chr04g0258801' => 'lal', 'Lalb_Chr05g0217531' => 'lal', 'Lalb_Chr07g0188061' => 'lal', 'Lalb_Chr09g0326781' => 'lal', 'Lalb_Chr12g0209241' => 'lal', 'Lalb_Chr13g0293171' => 'lal', 'Lj1C1228T8' => 'lonja', 'Lj2A270G30' => 'lonja', 'Lj2g0026430' => 'lja', 'Lj3C853T17' => 'lonja', 'Lj4g0012349' => 'lja', 'Lj4g0018743' => 'lja', 'Lj4g0025991' => 'lja', 'Lj5A239T82' => 'lonja', 'Lj6C724G8' => 'lonja', 'Lj6g0027949' => 'lja', 'Lsat_1_v5_gn_3_113501' => 'lsa', 'Lsat_1_v5_gn_3_27521' => 'lsa', 'Lsat_1_v5_gn_3_50140' => 'lsa', 'Lsat_1_v5_gn_4_26180' => 'lsa', 'Lsat_1_v5_gn_4_59981' => 'lsa', 'Lsat_1_v5_gn_5_107901' => 'lsa', 'Lsat_1_v5_gn_7_17520' => 'lsa', 'Lsat_1_v5_gn_8_32820' => 'lsa', 'Lsat_1_v5_gn_9_117100' => 'lsa', 'Manes.07G031600' => 'mes', 'Manes.10G068000' => 'mes', 'Manes.16G009700' => 'mes', 'Manes.17G037400' => 'mes', 'Mapoly0007s0062' => 'mpo', 'MBI02_g28327_MAGBIO' => 'mbi', 'MBI02_g35757_MAGBIO' => 'mbi', 'MBI03_g22271_MAGBIO' => 'mbi', 'MBI06_g12308_MAGBIO' => 'mbi', 'MBI18_g24802_MAGBIO' => 'mbi', 'MCO13G069' => 'mco', 'MD05G1044400' => 'mdo', 'MD05G1343500' => 'mdo', 'MD10G1051600' => 'mdo', 'MD10G1318600' => 'mdo', 'MD13G1009600' => 'mdo', 'MD16G1008000' => 'mdo', 'Medtr1g033830' => 'mtr', 'Medtr2g022880' => 'mtr', 'Medtr4g094212' => 'mtr', 'Medtr4g131930' => 'mtr', 'MELO3C002468.2' => 'cme', 'MELO3C018638.2' => 'cme', 'MELO3C020276.2' => 'cme', 'MELO3C022598.2' => 'cme', 'MELO3C028931.2' => 'cme', 'Migut.E00594' => 'egut', 'Migut.E00659' => 'egut', 'Migut.H01564' => 'egut', 'Migut.M01301' => 'egut', 'MSTRG.13146' => 'ama', 'MSTRG.13664' => 'ama', 'MSTRG.14641' => 'ama', 'MSTRG.2083' => 'ama', 'Nitab4.5_0000129g0440' => 'nta', 'Nitab4.5_0000944g0010' => 'nta', 'Nitab4.5_0000994g0040' => 'nta', 'Nitab4.5_0001619g0070' => 'nta', 'Nitab4.5_0002533g0100' => 'nta', 'Nitab4.5_0005531g0010' => 'nta', 'Nitab4.5_0007482g0070' => 'nta', 'Nitab4.5_0007973g0030' => 'nta', 'Nitab4.5_0010096g0030' => 'nta', 'Nitab4.5_0021613g0010' => 'nta', 'Nn1g00057' => 'nnu', 'Nn1g05367' => 'nnu', 'Nn1g07112' => 'nnu', 'Nn3g18703' => 'nnu', 'Nn4g22495' => 'nnu', 'Nn5g30091' => 'nnu', 'Oeu001134.2' => 'oeu', 'Oeu033194.1' => 'oeu', 'Oeu044056.1' => 'oeu', 'Oeu063905.2' => 'oeu', 'Os02g0683900' => 'osa', 'Os03g0120300' => 'osa', 'Os03g0565600' => 'osa', 'Os07g0102400' => 'osa', 'Os10g0537500' => 'osa', 'Peaxi162Scf00001g00030' => 'pax', 'Peaxi162Scf00097g02011' => 'pax', 'Peaxi162Scf00201g00082' => 'pax', 'Peaxi162Scf00203g01317' => 'pax', 'Peaxi162Scf00262g00615' => 'pax', 'Peaxi162Scf00329g00940' => 'pax', 'PGR004G1303' => 'pgr', 'PGR031G2208' => 'pgr', 'PGR042G1674' => 'pgr', 'PGR042G3163' => 'pgr', 'PGSC0003DMG400011291' => 'stu', 'PGSC0003DMG400012555' => 'stu', 'PGSC0003DMG400016376' => 'stu', 'PGSC0003DMG400016487' => 'stu', 'PGSC0003DMG400029437' => 'stu', 'PGSC0003DMG400031373' => 'stu', 'Phvul.002G186200' => 'pvu', 'Phvul.002G209600' => 'pvu', 'Phvul.003G013100' => 'pvu', 'Phvul.003G077400' => 'pvu', 'Potri.004G018100' => 'ptr', 'Potri.008G144400' => 'ptr', 'Potri.010G097900' => 'ptr', 'Potri.011G001000' => 'ptr', 'Pp3c1_42710' => 'ppa', 'Pp3c1_42740' => 'ppa', 'Pp3c2_8490' => 'ppa', 'PRCOL_00005243' => 'pco', 'Prupe.1G342900' => 'ppe', 'Prupe.4G023400' => 'ppe', 'Prupe.8G060200' => 'ppe', 'Psat1g181880' => 'psa', 'Psat4g007240' => 'psa', 'Psat6g095600' => 'psa', 'Psat7g087360' => 'psa', 'Psat7g099160' => 'psa', 'PSO063G4305' => 'pso', 'PSO135G1066' => 'pso', 'PSO210G5511' => 'pso', 'PSO781G0267' => 'pso', 'PSO782G3929' => 'pso', 'PSO832G4370' => 'pso', 'QL03p042001' => 'qlo', 'QL05p073612' => 'qlo', 'QL05p073976' => 'qlo', 'QL11p021264' => 'qlo', 'RcHm_v2.0_Chr4g0446101' => 'rch', 'RcHm_v2.0_Chr5g0003581' => 'rch', 'RcHm_v2.0_Chr5g0037351' => 'rch', 'Rhsim09G0075100' => 'rsi', 'Rhsim13G0155900' => 'rsi', 'Sabra04G0010000' => 'sbr', 'Sabra08G0109400' => 'sbr', 'Sabra11G0000400' => 'sbr', 'SalBow1G7691' => 'sbo', 'SalBow2G0452' => 'sbo', 'SalBow2G1881' => 'sbo', 'SalBow8G4247' => 'sbo', 'Sc03g0006190' => 'sci', 'Sc03g0008700' => 'sci', 'Sc08g0003460' => 'sci', 'Sc16g0006300' => 'sci', 'Sc17g0007250' => 'sci', 'Sed0009914' => 'sed', 'Sed0013941' => 'sed', 'Sed0018006' => 'sed', 'Sed0020436' => 'sed', 'Sed0026384' => 'sed', 'SEGI_00001' => 'sgi', 'SEGI_04826' => 'sgi', 'SEGI_32584' => 'sgi', 'SEGI_40610' => 'sgi', 'SGA_v2.0_scaffold4G01927' => 'sas', 'SGA_v2.0_scaffold65G22222' => 'sas', 'SGA_v2.0_scaffold89G27460' => 'sas', 'SGA_v2.0_scaffold8G04346' => 'sas', 'SMO119G0384' => 'smo', 'SMO203G0155' => 'smo', 'SMO347G0221' => 'smo', 'SMO351G0138' => 'smo', 'Solyc01g105270.4' => 'sly', 'Solyc02g080370.3' => 'sly', 'Solyc04g008540.3' => 'sly', 'Solyc09g005240.3' => 'sly', 'Solyc10g005270.1' => 'sly', 'Sopen01g003440' => 'spe', 'Sopen01g047770' => 'spe', 'Sopen02g025070' => 'spe', 'Sopen04g003700' => 'spe', 'Sopen10g001260' => 'spe', 'Sp1g12890' => 'spa', 'Sp2g13590' => 'spa', 'Sp7g19960' => 'spa', 'TAR177G0001' => 'tar', 'TAR381G0614' => 'tar', 'TAR622G1287' => 'tar', 'TAR625G1198' => 'tar', 'TAR627G0516' => 'tar', 'TAR629G0756' => 'tar', 'THA.LOC104801772' => 'tha', 'THA.LOC104805123' => 'tha', 'THA.LOC104812963' => 'tha', 'THA.LOC104813008' => 'tha', 'THA.LOC104824099' => 'tha', 'Thecc.02G138400' => 'tca', 'Thecc.02G311100' => 'tca', 'Thecc.06G217900' => 'tca', 'Thhalv10004674m.g' => 'esa', 'Thhalv10008286m.g' => 'esa', 'Thhalv10025897m.g' => 'esa', 'TPR.G11441' => 'tpr', 'TPR.G34764' => 'tpr', 'TPR.G35850' => 'tpr', 'TPR.G37025' => 'tpr', 'TPR.G37080' => 'tpr', 'TPR.G7269' => 'tpr', 'TPR.G7635' => 'tpr', 'TWI14G0700' => 'twi', 'TWI23G1257' => 'twi', 'TWI38G0653' => 'twi', 'TWI38G1274' => 'twi', 'TWI53G1271' => 'twi', 'TWI74G1452' => 'twi', 'unitig_0.g960' => 'ugi', 'unitig_744.g24522' => 'ugi', 'vmacro03696' => 'vma', 'vmacro10789' => 'vma', 'vmacro10790' => 'vma', 'vmacro19934' => 'vma', 'VMungo0251G0482' => 'vmu', 'VMungo0251G1860' => 'vmu', 'VMungo0251G3424' => 'vmu', 'VMungo1215G0319' => 'vmu', 'VMungo1215G0641' => 'vmu', 'Zm00001eb001520' => 'zma', 'Zm00001eb022120' => 'zma', 'Zm00001eb054750' => 'zma', 'Zm00001eb118330' => 'zma', 'Zm00001eb167970' => 'zma', 'Zm00001eb250780' => 'zma', 'Zm00001eb298130' => 'zma', 'Zm00001eb351290' => 'zma', 'Zm00001eb393720' => 'zma', 'Zm00001eb403790' => 'zma' ) $gf_id = 'HOM05D001248' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001248' ) $data_identifier = 'HOM05D001248' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 13, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 12, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 5, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 20, 'gra' => (int) 9, 'vvi' => (int) 8, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb403790' $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